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Boosting Virtual Screening Enrichments with Data Fusion: Coalescing Hits from Two-Dimensional Fingerprints, Shape, and Docking

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Flexible protein–ligand docking by global energy optimization in internal coordinates

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Automated docking of flexible ligands: Applications of autodock

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Comparison of 2D Fingerprint Methods for Multiple‐Template Similarity Searching on Compound Activity Classes of Increasing Structural Diversity

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Integrated Modeling Program, Applied Chemical Theory (IMPACT)

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A Role for Hydration in Interleukin‐2 Inducible T Cell Kinase (Itk) Selectivity

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Inhibition of protein–protein interactions: The discovery of druglike β‐catenin inhibitors by combining virtual and biophysical screening

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Enhancing the Effectiveness of Ligand‐Based Virtual Screening Using Data Fusion

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Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen

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PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results

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Epik: a software program for pK a prediction and protonation state generation for drug-like molecules

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What do we know and when do we know it?

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Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide

inferredcites →https://doi.org/10.1007/s10822-013-9644-8openalex-snapshot

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

inferredcites →https://doi.org/10.1007/s11030-006-9039-zopenalex-snapshot

Reverse fingerprinting, similarity searching by group fusion and fingerprint bit importance

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Virtual screening and bioassay study of novel inhibitors for dengue virus mRNA cap (nucleoside-2′O)-methyltransferase

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Consensus scoring for protein–ligand interactions

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Ultrafast shape recognition: Evaluating a new ligand-based virtual screening technology

inferredcites →https://doi.org/10.1016/j.jmgm.2010.05.008openalex-snapshot

Analysis and comparison of 2D fingerprints: Insights into database screening performance using eight fingerprint methods

inferredcites →https://doi.org/10.1016/s0022-2836(95)80037-9openalex-snapshot

Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation

inferredcites →https://doi.org/10.1016/s1093-3263(01)00125-5openalex-snapshot

Consensus scoring for ligand/protein interactions

inferredcites →https://doi.org/10.1021/ci00051a005openalex-snapshot

Implementation of nonhierarchic cluster analysis methods in chemical information systems: selection of compounds for biological testing and clustering of substructure search output

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How Does Consensus Scoring Work for Virtual Library Screening? An Idealized Computer Experiment

inferredcites →https://doi.org/10.1021/ci025596jopenalex-snapshot

Combination of Fingerprint-Based Similarity Coefficients Using Data Fusion

inferredcites →https://doi.org/10.1021/ci030004yopenalex-snapshot

Finding Multiactivity Substructures by Mining Databases of Drug-Like Compounds

inferredcites →https://doi.org/10.1021/ci049615wopenalex-snapshot

Analysis of Data Fusion Methods in Virtual Screening: Theoretical Model

inferredcites →https://doi.org/10.1021/ci0496797openalex-snapshot

LINGO, an Efficient Holographic Text Based Method To Calculate Biophysical Properties and Intermolecular Similarities

inferredcites →https://doi.org/10.1021/ci050034wopenalex-snapshot

Consensus Scoring Criteria for Improving Enrichment in Virtual Screening

inferredcites →https://doi.org/10.1021/ci050283kopenalex-snapshot

Comparison of Consensus Scoring Strategies for Evaluating Computational Models of Protein−Ligand Complexes

inferredcites →https://doi.org/10.1021/ci050296yopenalex-snapshot

The Use of Consensus Scoring in Ligand-Based Virtual Screening

inferredcites →https://doi.org/10.1021/ci050348jopenalex-snapshot

New Methods for Ligand-Based Virtual Screening: Use of Data Fusion and Machine Learning to Enhance the Effectiveness of Similarity Searching

inferredcites →https://doi.org/10.1021/ci100015jopenalex-snapshot

ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers

inferredcites →https://doi.org/10.1021/ci100062nopenalex-snapshot

Large-Scale Systematic Analysis of 2D Fingerprint Methods and Parameters to Improve Virtual Screening Enrichments

inferredcites →https://doi.org/10.1021/ci100436popenalex-snapshot

FRED Pose Prediction and Virtual Screening Accuracy

inferredcites →https://doi.org/10.1021/ci2002704openalex-snapshot

Rapid Shape-Based Ligand Alignment and Virtual Screening Method Based on Atom/Feature-Pair Similarities and Volume Overlap Scoring

inferredcites →https://doi.org/10.1021/ci2004835openalex-snapshot

Virtual Screening Data Fusion Using Both Structure- and Ligand-Based Methods

inferredcites →https://doi.org/10.1021/ci200528dopenalex-snapshot

Recognizing Pitfalls in Virtual Screening: A Critical Review

inferredcites →https://doi.org/10.1021/ci300547gopenalex-snapshot

Combination of Similarity Rankings Using Data Fusion

inferredcites →https://doi.org/10.1021/ci4000147openalex-snapshot

Structure-Based Virtual Screening of MT2 Melatonin Receptor: Influence of Template Choice and Structural Refinement

inferredcites →https://doi.org/10.1021/ci600426eopenalex-snapshot

Evaluating Virtual Screening Methods: Good and Bad Metrics for the “Early Recognition” Problem

inferredcites →https://doi.org/10.1021/ci6004993openalex-snapshot

Supervised Consensus Scoring for Docking and Virtual Screening

inferredcites →https://doi.org/10.1021/ci700052xopenalex-snapshot

Comparison of Topological, Shape, and Docking Methods in Virtual Screening

inferredcites →https://doi.org/10.1021/ci7004498openalex-snapshot

Application of Belief Theory to Similarity Data Fusion for Use in Analog Searching and Lead Hopping

inferredcites →https://doi.org/10.1021/ci8004226openalex-snapshot

How To Optimize Shape-Based Virtual Screening: Choosing the Right Query and Including Chemical Information

inferredcites →https://doi.org/10.1021/ci960373copenalex-snapshot

The Information Content of 2D and 3D Structural Descriptors Relevant to Ligand-Receptor Binding

inferredcites →https://doi.org/10.1021/ci990086jopenalex-snapshot

Comparison of 2D Fingerprint Types and Hierarchy Level Selection Methods for Structural Grouping Using Ward's Clustering

inferredcites →https://doi.org/10.1021/ct900587bopenalex-snapshot

Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field

inferredcites →https://doi.org/10.1021/ja00214a001openalex-snapshot

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin

inferredcites →https://doi.org/10.1021/jm010548wopenalex-snapshot

Molecular Docking and High-Throughput Screening for Novel Inhibitors of Protein Tyrosine Phosphatase-1B

inferredcites →https://doi.org/10.1021/jm011112jopenalex-snapshot

Successful Virtual Screening for Novel Inhibitors of Human Carbonic Anhydrase: Strategy and Experimental Confirmation

inferredcites →https://doi.org/10.1021/jm020406hopenalex-snapshot

Surflex: Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine

inferredcites →https://doi.org/10.1021/jm030605gopenalex-snapshot

Efficient Method for High-Throughput Virtual Screening Based on Flexible Docking: Discovery of Novel Acetylcholinesterase Inhibitors

inferredcites →https://doi.org/10.1021/jm0306430openalex-snapshot

Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy

inferredcites →https://doi.org/10.1021/jm030644sopenalex-snapshot

Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening

inferredcites →https://doi.org/10.1021/jm040163oopenalex-snapshot

A Shape-Based 3-D Scaffold Hopping Method and Its Application to a Bacterial Protein−Protein Interaction

inferredcites →https://doi.org/10.1021/jm049933mopenalex-snapshot

An In Silico Approach to Discovering Novel Inhibitors of Human Sirtuin Type 2

inferredcites →https://doi.org/10.1021/jm049970dopenalex-snapshot

Combination of a Naive Bayes Classifier with Consensus Scoring Improves Enrichment of High-Throughput Docking Results

inferredcites →https://doi.org/10.1021/jm050468iopenalex-snapshot

Scaffold Hopping through Virtual Screening Using 2D and 3D Similarity Descriptors: Ranking, Voting, and Consensus Scoring

inferredcites →https://doi.org/10.1021/jm050540copenalex-snapshot

Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects

inferredcites →https://doi.org/10.1021/jm051256oopenalex-snapshot

Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein−Ligand Complexes

inferredcites →https://doi.org/10.1021/jm060023+openalex-snapshot

Discovery of a Nanomolar Inhibitor of the Human Murine Double Minute 2 (MDM2)−p53 Interaction through an Integrated, Virtual Database Screening Strategy

inferredcites →https://doi.org/10.1021/jm0608356openalex-snapshot

Benchmarking Sets for Molecular Docking

inferredcites →https://doi.org/10.1021/jm0700971openalex-snapshot

P2Y1 Antagonists: Combining Receptor-Based Modeling and QSAR for a Quantitative Prediction of the Biological Activity Based on Consensus Scoring

inferredcites →https://doi.org/10.1021/jm7012425openalex-snapshot

Discovery of Novel Agonists and Antagonists of the Free Fatty Acid Receptor 1 (FFAR1) Using Virtual Screening

inferredcites →https://doi.org/10.1021/jm701248topenalex-snapshot

Docking Study Yields Four Novel Inhibitors of the Protooncogene Pim-1 Kinase

inferredcites →https://doi.org/10.1021/jm990352kopenalex-snapshot

Consensus Scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures into Proteins

inferredcites →https://doi.org/10.1021/jp003919dopenalex-snapshot

Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides

inferredcites →https://doi.org/10.1021/jp3003992openalex-snapshot

Exploring Protein Flexibility: Incorporating Structural Ensembles From Crystal Structures and Simulation into Virtual Screening Protocols

inferredcites →https://doi.org/10.1093/bioinformatics/btl155openalex-snapshot

Query Chem: a Google-powered web search combining text and chemical structures

inferredcites →https://doi.org/10.1111/j.1747-0285.2005.00327.xopenalex-snapshot

Use of an Induced Fit Receptor Structure in Virtual Screening

inferredcites →https://doi.org/10.1111/j.1747-0285.2012.01396.xopenalex-snapshot

Generation of Receptor Structural Ensembles for Virtual Screening Using Binding Site Shape Analysis and Clustering

inferredcites →https://doi.org/10.2174/0929867013372481openalex-snapshot

Pharmacophore Modeling and Three-dimensional Database Searching for Drug Design Using Catalyst

inferredcites →https://doi.org/10.2174/1381612053507549openalex-snapshot

New Methodologies for Ligand-Based Virtual Screening

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Structural Refinement of 2,4-Thiazolidinedione Derivatives as New Anticancer Agents Able to Modulate the BAG3 Protein

inferred← citeshttps://doi.org/10.35537/10915/51575openalex-snapshot

Topología molecular aplicada a la búsqueda de nuevos fármacos para el tratamiento de la epilepsia refractaria

inferred← citeshttps://doi.org/10.35537/10915/57704openalex-snapshot

Topología molecular aplicada al reconocimiento de sustratos de la Proteína de Resistencia del Cáncer de Mama (BCRP)

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